I've RNA seq, Human, Paired-end data, Sample size is <40. These are aligned using STAR, RSEM processed. With RSEM I've TPM and expected counts, that is two files columns as individual IDs and row as gene names.
I'm interested to normalize gene data. With edgeR tutorial (link in the end) and few other online resources I see that after following steps there's an R object that contains
norm.factors (Page 15) value for each individual.
I'm unable to wrap my head around it, now. If I'm interested to get normalized gene counts, can I go ahead and multiple each individual's norm.factor into its gene counts? For example, the expected count for
Gene1 is 100 and it's
0.80, can I say that the normalized gene count is
I'm not interested to perform voomm, or differential expression analysis.
Follow up question: If I'm to sample few individuals' data from these RNA-seq should I
a) normalize all together and extract interested individuals, or,
b) extract interested individuals and then perform normalization.
I think since normalization uses per person library size, each person's normalization is independent of the others. Can someone please correct me if I'm wrong?